L519:  Lab Session 9 (11/4/05)

Today's Topics

• Motif Discovery
• MEME
• Gibbs sampler
• Logos

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¤ Motif Discovery

• Useful introductions to motif discovery
• PPT1 - Local Multiple Sequence Alignment Motif Discovery
• PPT2 - DNA Motif Finding (By Katherina Kechris)
• PPT3 - Introduction to Gibbs Sampling 

¤ MEME - Multiple EM for Motif Elicitation

• Employing maximum expectation method.
• Comprehensive manual for Gibbs sampler
• MEME homepage at SDSC
• MEME: For discoverying motifs (highly conserved regions)
• MAST: For searching sequence databases using motifs
• Sample MEME output
• Download MEME source codes
• MEME paper, MAST paper
• Try the sample sequence on their website. Result

• SAMPLE SEQUENCES: /tmp/L519FALL2005/Lab9/  (Copy to your own directory)
•  
• COMMENTS: MEME generates output in html by default.
• COMMENTS: "-dna" option should be used for DNA sequences.
• COMMENTS: MEME encounters an error if you run MEME on a directory without write permission.
  "meme.usage.29999.tmp: Permission denied."
   
• > meme COG0001.fas
• > meme COG0001.fas -text
• > meme COG0001.fas -protein -nmotifs 2
• > meme ProtSeq.fas -protein -minw 10 -maxw 20 -nmotifs 3 > ProtSeq.meme.html

 

¤ Gibbs motif sampler

• Employing gibbs sampling algorithm
• Gibbs sampler webpage
• Web Gibbs sampler for DNA
• Web Gibbs sampler for protein
• Local version (Add the path to $PATH in your .bashrc file)
• New version : /usr/local/dna/bin/Gibbs
• More options
• Old version : /usr/local/bio/bin/gibbs
• COMMENTS: "-n" option should be used for DNA sequences.
• Basic usage
  > gibbs <file> motif_lengths [options]
• Sample usage
  >gibbs COG0001.fas 15
  >gibbs COG0001.fas 7,15
  >gibbs COG0001.fas 15 5
  >gibbs ProtSeq.fas 10,20 > ProtSeq.gibbs.out
  >Gibbs ProtSeq.fas 10,20 > ProtSeq.Gibbs.out

• Compare performance of new Gibbs with old gibbs
• > Gibbs COG0001.fas 15 -o COG0001.Gibbs.out
  > gibbs COG0001.fas 15 > COG0001.gibbs.out
   
• Save the model with -f option and search using 'scan'
  > gibbs COG0001.fas 15 -f
  > Gibbs COG0001.fas 15 -N COG0001.fas.sn
  > /usr/local/bio/bin/scan COGSET COG0001.fas.sn > COGSET.scan.out

 

¤ Logos

• Web version Logo
• Source code
• Sample Sequence
• Logo Result

• Standalone version
• Download the source code. Uncompress the .tar.gz archive and you can directly run the 'seqlogo' program.
• ./seqlogo -f seq.fas > seq.eps
• ./seqlogo -F PDF -f seq.fas -c > seq.pdf
• ./seqlogo -F GIF -f seq.fas > seq.gif 
• If this doesn't work, first convert to .eps and then use 'convert' program
• convert seq.eps seq.gif     

 

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Last Modified : November 3, 2005

Maintained by : Junguk Hur ()